The second area is done, at least the map and tiles. There are some scripting events to be done and tweaked. Right now I'm preparing the tilesets for the third area. Just as many of you suggested, the ruins will be some kind of industrial/mining facilities.
Here is a snapshot of the caves before the third area, this shows the new tile color palette. The background will be properly replaced soon.
Alpha Metroids are being tweaked and improved all the time. Currently they have the normal introductions done (normal and coming out of the cocoon), I'll be adding more these days.
Sound production is becoming really funny. In order to do some cool screeching sounds for the different Metroid evolutions, me and a friend are recording some really weird screams here at the studio, and then applying a lot of effects. I'm ripping sounds from plenty of games too, sound test in emulators are really useful. These will be used to create new sounds for the game.
Music production has also begun, there's still a long way to complete the soundtrack.
Thanks everybody for your comments and suggestions, I really appreciate them.